BLASTP 2.2.18 [Mar-02-2008]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 0001.0390.p
         (346 letters)

Database: BlastDatabases/690/690 
           3295 sequences; 1,000,347 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|134093535|ref|YP_001098610.1| tRNA-dihydrouridine synthase B ...   519   e-149
gi|134095593|ref|YP_001100668.1| tRNA-dihydrouridine synthase A ...    88   6e-19

>gi|134093535|ref|YP_001098610.1| tRNA-dihydrouridine synthase B
           [Herminiimonas arsenicoxydans]
          Length = 322

 Score =  519 bits (1337), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 258/318 (81%), Positives = 282/318 (88%)

Query: 21  MAGVTDRPFRQLCKQLGAGYAVSEMAASDPRLWHSEKTSRRINHDGEMEPKAVQIAGADP 80
           MAGVTDRPFRQLCKQLGAGYAVSEMAAS+PRLW ++K++RR NHDGE+EPKAVQIAGADP
Sbjct: 1   MAGVTDRPFRQLCKQLGAGYAVSEMAASNPRLWATDKSTRRTNHDGEVEPKAVQIAGADP 60

Query: 81  AMLADCAKYNVERGAQIIDINMGCPVKKVCNSWCGSALLQDEELVARILDAVVSAVDVPV 140
            MLA+CAK+NV+RGAQIIDINMGCPVKKVCNSWCGSALLQ E LVA IL AVV+AVDVPV
Sbjct: 61  LMLAECAKFNVDRGAQIIDINMGCPVKKVCNSWCGSALLQHESLVAEILQAVVAAVDVPV 120

Query: 141 TLKFRTGWNRANKNALKIAARAEAAGIAMLTLHGRTRADGYSGEAEYETIAAVKAAVKIP 200
           TLKFRTGW+RA+KNAL IA  AE +GIAMLTLHGRTRADGYSGEAEYE IAAVKAAV IP
Sbjct: 121 TLKFRTGWDRAHKNALNIARIAEQSGIAMLTLHGRTRADGYSGEAEYEMIAAVKAAVSIP 180

Query: 201 VVANGDITTPEKAREVLRITGADAVMVGRAAQGRPWIFREIDHFLRTGDFLPAPLVSEVE 260
           VVANGDITTPEKA+ VL  TGADA+M+GRAAQGRPWIFREI H+LRTG  LPAPL+SEV 
Sbjct: 181 VVANGDITTPEKAKFVLEATGADAIMIGRAAQGRPWIFREIVHYLRTGTHLPAPLISEVR 240

Query: 261 HLMAEHLQAHYAFYGEYLGVRTARKHIGWYVRDLPGGEQFRRSMNRIEDCGQQLQAVRQF 320
            LM EHL+AHYAFYGEYLGVRTARKHIGWYVR+L  GE FR+ MNR+EDC QQL AV +F
Sbjct: 241 TLMDEHLRAHYAFYGEYLGVRTARKHIGWYVRELIDGEAFRQQMNRLEDCAQQLAAVNEF 300

Query: 321 FADQAAHGERLQYERAQE 338
           F  Q  HGERLQY   +E
Sbjct: 301 FELQLTHGERLQYRPTEE 318


>gi|134095593|ref|YP_001100668.1| tRNA-dihydrouridine synthase A
           [Herminiimonas arsenicoxydans]
          Length = 338

 Score = 88.2 bits (217), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 84/310 (27%), Positives = 141/310 (45%), Gaps = 22/310 (7%)

Query: 13  RNNVFVAPMAGVTDRPFRQLCKQLG-AGYAVSEMAASDPRLWHSEKTSRRINHDGEMEPK 71
           +  V VAPM   TDR  R   +Q+    +  +EM  +   L H +  SR ++ + E  P 
Sbjct: 8   KRRVSVAPMMDWTDRHCRMFHRQITRHTWFYTEMVTTGA-LLHGD-VSRHLDFNHEEHPV 65

Query: 72  AVQIAGADPAMLADCAKYNVERGAQIIDINMGCPVKKVCNSWCGSALLQDEELVARILDA 131
           A+Q+ G++PA LA  AK   + G   I++N GCP ++V     G+ L+ +  LVA  + A
Sbjct: 66  ALQLGGSEPADLAKSAKLGEQWGYDEINLNCGCPSERVQKGAFGACLMNEAALVADCVKA 125

Query: 132 VVSAVDVPVTLKFRTGWNR-ANKNALK-IAARAEAAGIAMLTLHGRTRA-DGYSGEAE-- 186
           +  AV + VT+K R G +  A+ + ++        AG     +H R     G S +    
Sbjct: 126 MRDAVQIDVTVKHRIGIDDIASYDFVRDFVGTVAEAGCNTFIVHARNAVLKGLSPKENRE 185

Query: 187 -----YETIAAVKAAV-KIPVVANGDITTPEKAREVLRITGADAVMVGRAAQGRPWIFRE 240
                YE    +K    ++ ++ NG I T   A     +   D VM+GR A   P++   
Sbjct: 186 IPPLRYEFAYQLKQDFPQLEIIINGGIKT--LAEIDTHLVHVDGVMLGREAYHNPYLMSA 243

Query: 241 IDHFLRTGDFLPAPLVSEVEHLMAEHLQAHYAFYGEY-----LGVRTARKHIGWYVRDLP 295
            D     GD       ++V H M  +++A    +G+      L + +  +H+   +  LP
Sbjct: 244 FDARY-YGDIAAPKSRAQVLHAMLPYIRAQLELHGKSEKGGGLRLNSITRHMLGLMAGLP 302

Query: 296 GGEQFRRSMN 305
               FR+S++
Sbjct: 303 NARGFRQSLS 312


  Database: BlastDatabases/690/690
    Posted date:  Apr 9, 2011  4:48 AM
  Number of letters in database: 1,000,347
  Number of sequences in database:  3295
  
Lambda     K      H
   0.321    0.135    0.405 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3295
Number of Hits to DB: 613,520
Number of extensions: 23232
Number of successful extensions: 70
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 68
Number of HSP's successfully gapped: 2
Length of query: 346
Length of database: 1,000,347
Length adjustment: 82
Effective length of query: 264
Effective length of database: 730,157
Effective search space: 192761448
Effective search space used: 192761448
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 129 (54.3 bits)